Changing Bodies
by Madi92
Summary: They come back from the mission and everything was fine, till next morning. Due to something SGA-1 turned on, John and Elizabeth change bodies to feel what the other one has to go through. If this wasn't enough, enemy are knocking to their doors and Atlantis is once again in danger. Rated T.
1. Chapter 1

**A/N:** _Here is something new. Of course John/Elizabeth parring :)_

_Enjoy!_

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Elizabeth slowly opened her sleepy eyes with a big yawn just to find herself not in her room, but John Sheppard's.

'Oh God. How this happened? Did we sleep together? I hope not! I don't remember a thing from last night, except for major headache.' She thought getting out of the bed.

The chilly air in the room gave her a goose flesh, so she took a sheet which she found on the floor and precisely wrapped it around her body. Then she realized another thing; it wasn't her feminine body but very, very male one. Elizabeth hold her breath and biting her up lip, she looked down.

'Yep, I'm definitely a man. Please let it be only a bad dream. Please, please…'

She quickly walked into bathroom and stopped by the sink; she splashed her face with very cold water and as she looked into mirror, her horror came back. She indeed was in a man body, and if it wasn't enough for today, it was John Sheppard's!

'No, no, no. It's not happening, not to me! Why, for crying a loud, in two galaxies it has to be me to turn into him?' Elizabeth took a step back, as she was rethinking this whole messy situation. 'I'm John, so he has to be me, right? I mean he, if we did _it _yesterday, must be here, right?'

She looked around the bathroom and when she found the clean underwear in the drawer, she put it on and then made her way back to room. Tiptoeing, she walked to the bed looking at the body, which was lying on her pillow right now, she slowly put a hand on the body and pinched it; person stirred. It wasn't her, her body with John inside, but another woman. Elizabeth swallowed and crossed her arms on a chest watching closely as the woman wake up.

"Johnny, my darling, come back to bed." She heard husky and sexy voice of the woman.

"No." Elizabeth said trying not to look down at the naked woman in front of her. "It's time for you to leave, doctor Nowacki."

"Johnny?"

"It's over. I don't have time for relationships; I have to focus on my work."

"Who says something about relationship, Johnny. It's just a mind-blowing sex, my darling."

Mary-Jane Nowacki gave Elizabeth seductive smile but as she saw the look on John's face, she gave up; slowly she got out of the bed and stopped in front of her lover, naked. Dr Weir rolled her eyes and opened the door, taking all of Mary-Jane clothes from the floor; she thrown them at her and once again, she politely asked her to leave. This time John's lover did as she was said and left Elizabeth all alone with her thoughts. As soon as the door closed, she reached for a com device from the coffee table and called John. After third time, as she was about to walked out and look for him, her com device responded.

"What did you do this time Colonel!?" she said with anger.

"Elizabeth, why are you screaming at me? Please my head…" John opened his sleepy eyes and slowly reached to his forehead and rubbed it. "What gave you the idea that I did something?"

"Well, get up of MY bed and take a look into mirror? You will see what gave me THAT idea!"

"Fine, fine…" he muttered not really thinking about what she said. John got up and walked into the bathroom. He turned on the lights and stopped in front of the mirror, he looked at it. His first reaction was screaming; he started touching his face. "I…I am you…"

"Exactly. Now tell me what did you do this time?

"I did nothing, I swear." He said still looking with amaze on his new body. "But how cool it is, Liz… I have boobs!"

"Don't you dare touching them, John Sheppard. You hear me, don't you dare!"

"Yeah, sure. Bye Elizabeth." He disconnected the com, focusing all his attention to Elizabeth, or right now his breast.

Dr. Weir took quick shower and knowing, that she will have to be John today, or a matter of facts till the moment they fix this, she put some clothes on herself and left the room heading to her office. She will have to help John, after all he will be running the whole city today, all by himself, and she knew that would be a totally disaster. She took a shortcut to control room, and then she walked into the transporter. The door was about to close, but in that moment Ronnon hold them, walking into.

"Sheppard what are you doing here so early?" he asked in surprise. Elizabeth swallowed and cleared her throat.

"Eee… I have to talk to doctor Weir." She pushed the control room dot on the pad and the transporter disappeared, few seconds later they were in the hallway next to the control room.

"Is she still chasing you after those mission reports? I recorded her everything on this." He said taking from his pants a small voice recorder. "You going to her anyway, can you give it to Weir?"

"Sure."

"Oh and remember about our little sparing at 10. I will be waiting for you and this time… be there!" he said clapping Elizabeth's shoulder before he disappeared into next hallway.

_Great. Sparing with Ronnon. He will absolutely kill me there._ She whispered continuing her way out of the control room.

As she got there, Elizabeth said hello to all the personnel before she walked into her office. She sat down on the chair looking at her usual spot by the desk. Report which she was holding she put with the voice recorder from Ronnon next to her tablet on the files 'to do' and she waited for John. Twelve minutes later she heard the door behind her opened, as she turned her head she saw herself; well technically she only saw John in her body. Elizabeth bit her lip as John sat down on her 'leader chair' with a big grin on his, hers face.

"What are you smiling at?" she said. "Is it funny? Really John I swear if we only find a way out of this mess, you are done! I'm sick of this, of all your mistakes, of this attitude; everything is fun for you. Could you take this mission, Atlantis, me and everybody here seriously? No, because you are only a child in side of man body, John." Elizabeth stood up. Before she took a step toward the door, John grabbed her arm. "At least try to behave like me until we find a solution for this. Doctor Beckett is not getting back from his mission for another day, but as soon as he steps through the stargate you and I with doctor McKay will solve this!

"Ok, I'm gonna try…"

"You are in charge of my city now. Don't mess it up or you will find yourself back on Earth as soon as you will be you again!"

Elizabeth left John all alone in her office and she walked to his room to change. It was time for her for sparring with Ronnon. As scared as she was for her life, she knew she has to do this. And besides for one day she will be John Sheppard, so she could not give a fuck about everything. It was her time to relax, before she will be herself again; tired and workaholic Elizabeth Weir, leader of the Ancient's city. She change her clothes and grabbed a bag before she walked out of the room and headed to the transporter.

She looked at the time; it was quarter to ten as she enter the gym and found it empty. Elizabeth put her bag on the floor and sat down next to the window. As she was waiting for Ronnon, she took some time to look at her magnificent city and think about this entire situation. She woke up as a man, as a John Sheppard! This wasn't normal situation, not even to them, to Atlantis…

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**TBC **

_so tell me what do you think? Should I continue this one?_


	2. Chapter 2

**_A/N: I would like to thank for all the reviews and I'm sorry it took me so long to publish and bad news is that the next chapters will take some time, 'coz they are not ready yet. Due to dead of my close family member I was unable to wrote more than two words. I wanted to apologize to everybody who reads this story, I will get back to writing it as soon as I will get over after grieving. For now I am giving you a chapter I wrote some time ago. Enjoy this one!_**

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"Any changes?" she asked walking to the control room. Elizabeth looked at the solid mysterious metal circle which was quietly standing on the floor.

"Sorry dr Weir. They still haven't checked in and didn't respond for any of our calls. It's been eight hours and twenty two minutes since Colonel Sheppard's team should come back."

"Fine, then. Contact Major Lorne and tell him to come back. We will send another rescue team later." she said and without further words she walked into her office.

Her professional poker face look was fast disappearing; the team she send for a simple recon was late and it didn't help that the one of team member was John. She was worried twice than always. Elizabeth looked at the stargate taking a deep breath to calm her nerves. She was about to turn her head when the magnificent ring came into live; the symbols started to glow and soon everyone saw a blue bubble which changed into puddle.

"Incoming wormhole. It's SGA-1's IDC."

"Let them in."

"Yes ma'am"

Chuck opened the iris and soon the whole unharmed SGA-1 walked into the stargate room. Elizabeth in the meantime walked to the stairs; by the way she was making steps you could tell she is furious, she stopped before the steps started fall down to the floor in the room under, crossing her arms on a chest she was observing. McKay was snuffling, while he was giving back his equipment to one of the apprentice from scientist department. Teyla surrounded by two Athosian; she recognize Haling; was deep in conversation with them. Ronon was talking something to John, the two of them clearly have a good time. Dr Weir gasped glaring.

"John Sheppard! To my office, now!" She said calmly, but her voice was fuming.

Elizabeth didn't even look at him, slowly she turned back and took step by step to her office. John gave his gear to the airman and shyly smiled to the rest of the team, before he followed Elizabeth. They walked into her office and as she comfortably sat down in her chair behind the desk, she looked at John.

"So what is it all about?" he asked with his cocky grin like nothing really happened. Or maybe he knew that this smile with gorgeous puppy eyes can melt Elizabeth's heart.

"You don't know? Really you don't know, Colonel?" she started. "Look at the time!"

"So we were late few minutes, so what…"

"Late? Few minutes?" she raised her eyebrow. "John not few minutes but over eight hours. I send two search teams for you. You weren't responding for our calls and didn't even bother to check in, Colonel. What you have to say for your defense?"

"Well, we might change the planet while we were on the mission, but hey, nothing bad happened and we needed to check something the people said to us. Don't make it a big deal."

"Big deal? Well it's a big deal, Colonel." She flared up raising from the chair. Right now John knew how screwed this situation was. "You disobey the direct order from your superior officer and it's not the first time. But this time, Colonel, you were way out of line. My hands are tight, it's going to be in your files and I might add that the IOA will want you back in SGC for questioning. What is more your team is suspended from gate travels till further notice. Major Lorne will take your duties as the military commander from now on. You're dismissed!"

He saluted her for a first time ever, despised the fact they were friends, he felt like doing it. She sat down and soon she was looking at some files. John walked to the door and when he was about to left her office, he heard her quite voice.

"Sometimes John I really wish you were me. And maybe in the situation like this, you would see how I am feeling, when one of our teams is not responding to calls and is coming back late." she sighed when he was walking through the door.

John stopped and looked at her. She was really worried about them, maybe even about him a little bit more. He walked away, knowing he disappointed her again and that his team will be waiting for him around the corner. And he wasn't mistaken; they were waiting for him, near the transporter. He smiled to them.

"So, what did she said?" Rodney asked.

"Not much. We're suspended till further notice, bla,bla,bla...same as always"

"John you do know, that what we did, wasn't fair toward Weir, and I truly understand her. We shouldn't go to this planet. It was not as much important…" said McKay, but unfortunately John interrupted her.

"Yeah but you had got new toys and maybe we will figure out from the writings on the cave where the ZPM is. She just overreacted, you'll see."

"I don't know John. Elizabeth is right. We should not go there without telling her. She is the leader." Teyla pointed out." I will try to talk to her, but if I was her I would be really mad and disappointed in you, Colonel."

"Oh for god's sake!" he said walking away. Right now he had enough this whole situation. He walked to his room and as soon as the door had closed behind him, John took his clothes off and naked he headed to the bathroom, to take a shower.

In the meantime Elizabeth was sitting in her office, her head buried in hands. She tried to focus on her work, but she couldn't; the report she was writing about John's little escapade had only a title for right now. She couldn't do it, she couldn't force herself to write a report which will be a one way ticket through the stargate on Earth and she knew that was her feelings toward him that was blocking her.

'I really suck at this. I let my personal feelings to cloud my judgment. I should be resigning from my office. I love him and I can't even hide it anymore. And now, I have to do what is right, but do I really want that high punishment for him? Did he really have to leave me and Atlantis?'

Dr Weir stood up and left the office heading to the balcony. Not this one next to the control room, no. She needed to be alone so she headed to South Pier to the groundbreaking stations. Walking down the hallways of Atlantis she calmed down, re-thought the entire situation.

'Listen to yourself Elizabeth… You're fooling yourself. He deserved for this, after what he has done. You can't leave it like this; he is always making his puppy eyes and your heart is melting. Not this time! If he's not sorry for his actions, he will be punish. So what he will be leaving Atlantis and probably marshal courted. Do you really want him screwing here everything? He doesn't fit here, never was and never will…'

The door had opened and she walked outside taking a deep breath, calmly she walked to the railing and looked at the ocean.

'It's not true. John FITS here, after all he has the Ancient's gene. He is half Ancient, half human, if anyone has the right to call Atlantis home, it's him. And after all he is very important member of my expedition, I was the one who took him here with me and I am responsible for his action. I did know about his past and well telling the truth I thought that somehow he will change for me, for Atlantis. I can't just send him back to Earth, he belongs here. Well but after what he has done he still needs to be punish. I will take care of that after the briefing, I do need to know every details before I make a decision what will happen next with my Colonel Sheppard!'

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**TBC**


	3. Chapter 3

She couldn't believe she survived sparing with Ronnon. Guess she still remembered some moves from her self defense lessons on which her father made her to go when she was in high-school. She was of course tired, no, she was exhausted but alive with one or two bruises here and there. No big deal, it will soon disappear. Besides it's not like it's her body after all.

"So how was your night, Sheppard?" Ronnon asked when the two of them were sitting on the floor in the gym.

"My night?"

"Yeah. I saw you with a woman." He said." You know dr Weir won't be happy if she see you parading all around the city with the hot member of her scientists department"

"What? Why?" She tried to sound like John, asking rather stupid questions. Ronnon smirked.

"Oh come on Shep. You didn't notice how she's looking at you?"

She shocked her head. 'Crap he knows about my little crash on John so that only means that everybody knows…'

"Well in that case you do need to be more focused on briefings. Get up man!"

She saw Ronnon stood up and took another kind of sticks for fight and throw one of them to Elizabeth. Another round sparring with him and she will be in the sickbay for sure so she got up and grab her bag.

"Sorry I have a meeting scheduled, but I'm sure Teyla..." Elizabeth saw the door are opening and Athosian leader went inside greetings them. It was her moment to escape, so she quickly made her way to the hallway, as she walked through the door, Elizabeth turned to face members of Colonel's team. "Play nice!" And Elizabeth was gone.

Dr Weir went to John's room, which taking their current situation, she was occupying for now. Her hand slowly shifted her palm through the panel next to the door and the room opened. She walked inside and then she realize she isn't alone; Sheppard was very comfortably sitting on the bed playing with her laptop. She closed the door behind her.

"What are you doing here?"she said.

"It's my room!"

"Well for this moment, it is not." Elizabeth put her bag on the chair next to the closet and made a few steps, she found herself next to the furniture. She opened the first drawer.

"Oh no! You won't be going through my underwear, Elizabeth." John quickly closed the drawer giving his boss one of those looks she was always using when Rodney wanted something; but it didn't work as he thought it would. Elizabeth raised her eyebrow as she opened a drawer again.

"Really John? And you hadn't done it?" It was rather a rhetorical question so she didn't waited for an answer but she was continuing. "I spend two hours working out with Ronnon. Two hours! My muscles hurts, I have bruises all over body and I'm sure I am not smelling very well. So right now I need a shower!"

She didn't wait for him to fight her back; she grabbed clean underwear from the drawer and clothes from another and headed to the bathroom. John followed her, opening the door in the same moment when she was taking off his T-shirt. At first Elizabeth didn't see him, but when she finally realize she is not alone, she stopped taking off hers clothes and glanced at John.

"What are you doing?"

"Oh come on it's my body and…"

"… and right now I am the one who is using it! So leave, please…"John didn't move so she continued. "John you do realize that I spend enough time as you so it's not like a didn't see your... hmm... oh for god's sake Colonel, you know exactly what I mean." she said.

When she saw smirk on his, well her face, Elizabeth throw the towel toward him telling him to get out. He did what she wanted and left; he walked back into the room and sat down on his bed. He waited and waited for her to walked out of his bathroom, but after fifteen minutes he got bored so he started going through her computer, trying to find some decent game. And he did found one of the classic 'shooting to aliens' game. He didn't realize when she walked in and looked at the screen.

"What are you doing?"

"I'm trying to beat your score." He said not to taking his eyes away from a laptop. "Really, 'Liz'beth I didn't know you are a big fan of computer games."

"I'm not, but some of the conference I had been attending were, let's just say I needed something to keep me awake." She said sitting down on the bed next to John in half lying position, her head leaned back against the wall.

"Well if you want you can shooting aliens down in reality. There you would never beat me down." He said looking at her after the game over.

"Guns are off limits for me." She said and then she continued flirtatiously."Why John Sheppard, are you proposing something, a little game tournament perhaps?

"I mean Jumpers, but never mind…" He started the game once again.

"Wait a minute… You mean Jumpers as the spaceships, Puddle Jumpers from Atlantis…" Her face started to brighten up as she slowly moved to the edge of the bed. "I am you right now… Do you think there might be a slight possibility that I can operate Ancient's technology?"

"Yhm… yeah" He answered not really bothering to look at her. But few second later it hit him, if she was thinking about the same thing as he did, he need to stop her before it's too late.

He quickly throw the laptop from his laps back to the bed and run after Elizabeth who had already left his room. It didn't took him long to catch her up, but even that didn't change her mind, she was still going or rather loudly jostling with John toward hangar bay. Elizabeth mainly because of the fact that she as the user of John's body was stronger and faster walked into the Jumper first and quickly sat down in the pilot seat. John followed her and took a seat next to her.

"Ok let's find out if it's true…"

"Oh so now you want to be a partner in the crime, seriously John!?"

" Come on, 'Liz'beth you know we never do something fun together. And besides you will need someone who actually knows how to fly this baby if you fell down from the sky." He grinned as she gave him one of her famous 'kill me now' looks. " I mean it's not like you going to crash the Jumper."

"You know John, it will be better if you shut up. Now!" He wanted to say something more but gave up after John looked at Elizabeth's angry face (well his angry face).


End file.
